What are the laboratory diagnosis guidelines for Carbapenem-Resistant Enterobacteriaceae (CRE) as per Clinical and Laboratory Standards Institute (CLSI) guidelines?

From the Guidelines

Laboratory diagnosis of Carbapenem-Resistant Enterobacterales (CREs) according to CLSI Guidelines M-100,2025 involves a stepwise approach focusing on phenotypic and genotypic methods, with a strong recommendation to use rapid testing strategies to identify specific carbapenemases and guide antibiotic therapy, as stated in the 2022 guideline endorsed by the Italian Society of Infection and Tropical Diseases (SIMIT) and others 1. The initial screening should be performed using carbapenem susceptibility testing, with isolates showing reduced susceptibility to ertapenem (MIC ≥0.5 μg/mL), meropenem (MIC ≥1 μg/mL), or imipenem (MIC ≥2 μg/mL) considered potential CREs. Some key points to consider in the diagnosis of CREs include:

• The use of phenotypic methods such as the modified carbapenem inactivation method (mCIM) to detect carbapenemase production, as recommended in the 2023 guidelines for the diagnosis, treatment, prevention, and control of infections caused by carbapenem-resistant Gram-negative bacilli 1.
• The importance of identifying specific carbapenemase genes (KPC, NDM, VIM, IMP, OXA-48-like) using molecular methods like PCR or whole genome sequencing, as emphasized in the 2022 guideline endorsed by SIMIT and others 1.
• The role of automated systems and commercial assays, such as immunochromatographic lateral flow assays, in providing rapid results within hours, as mentioned in the example answer.
• The need for accurate CRE identification to guide appropriate antimicrobial therapy selection, infection control measures, and epidemiological surveillance, as these organisms often carry resistance to multiple antibiotic classes beyond carbapenems, as highlighted in the 2022 guideline endorsed by SIMIT and others 1. It is worth noting that the 2009 guidance for control of infections with carbapenem-resistant or carbapenemase-producing Enterobacteriaceae in acute care facilities recommended the use of the modified Hodge test (MHT) to detect carbapenemases in isolates demonstrating elevated but susceptible carbapenem MICs 1. However, this recommendation is outdated compared to the more recent guidelines, which emphasize the importance of rapid testing strategies to identify specific carbapenemases and guide antibiotic therapy 1.

From the Research

Laboratory Diagnosis of CREs

As per CLSI Guidelines M-100,2025, the laboratory diagnosis of carbapenem-resistant Enterobacteriaceae (CRE) is crucial for infection control and patient care. The following methods are used for the detection of CRE:

• Phenotypic methods: These include Modified Hodge Test (MHT), Blue Carba test (BCT), Combined Disc Test (CDT), and The Carbapenem Inactivation Method (CIM) 2.
• Molecular methods: These include PCR sequencing and recombinase polymerase amplification combined with lateral flow strip (RPA-LFS) 3.

Phenotypic Methods

The performance of phenotypic methods for the detection of CRE has been compared in several studies:

• A study compared four phenotypic assays, including CDT, mCIM/eCIM, CARBA, and CDI, and found that CARBA and CDI were highly accurate, while CDT and mCIM/eCIM were moderately accurate 4.
• Another study found that CIM, MHT, and BCT correctly identified carbapenemase producers with sensitivity of 100%, 98%, and 90.8%, respectively 2.

Molecular Methods

Molecular methods, such as PCR sequencing and RPA-LFS, are also used for the detection of CRE:

• A study developed a rapid on-site visualization detection method for CPE using RPA-LFS, which could specifically differentiate four classes of carbapenemases without cross-reactivity 3.
• Another study reviewed the current state-of-art of carbapenemase detection methods, including phenotypic and molecular methods, and emphasized the importance of molecular characterization of carbapenemase genes by PCR sequencing 5.

Clinical Laboratory Detection

The clinical laboratory detection of CRE is crucial for patient care and infection control:

• A review article discussed the current phenotypic and molecular methods available to the clinical laboratory for the detection of CRE and emphasized the importance of evaluating carbapenemase production for infection control efforts 6.
• Another study highlighted the need for routine evaluation of carbapenem resistance mechanisms by the clinical laboratory, either in-house or by submitting isolates to a reference laboratory 6.